{"id":19740151,"url":"https://github.com/nceas/codyn","last_synced_at":"2025-04-30T05:32:49.690Z","repository":{"id":20432829,"uuid":"23709521","full_name":"NCEAS/codyn","owner":"NCEAS","description":"Community dynamics metrics","archived":false,"fork":false,"pushed_at":"2022-06-14T23:33:57.000Z","size":1169,"stargazers_count":32,"open_issues_count":11,"forks_count":8,"subscribers_count":16,"default_branch":"master","last_synced_at":"2024-04-25T20:21:08.150Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NCEAS.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-09-05T16:11:00.000Z","updated_at":"2023-12-28T04:25:28.000Z","dependencies_parsed_at":"2022-07-31T19:38:10.819Z","dependency_job_id":null,"html_url":"https://github.com/NCEAS/codyn","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCEAS%2Fcodyn","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCEAS%2Fcodyn/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCEAS%2Fcodyn/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NCEAS%2Fcodyn/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NCEAS","download_url":"https://codeload.github.com/NCEAS/codyn/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224198939,"owners_count":17272189,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-12T01:19:44.431Z","updated_at":"2024-11-12T01:19:45.618Z","avatar_url":"https://github.com/NCEAS.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# codyn - Community Dynamics Metrics\n\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/codyn)](https://cran.r-project.org/package=codyn)\n[![Build Status](https://travis-ci.com/NCEAS/codyn.png?branch=master)](https://travis-ci.com/NCEAS/codyn)\n![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/codyn)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n\n- **Authors**: Lauren Hallett [lauren.m.hallett@gmail.com], Meghan Avolio [meghan.avolio@jhu.edu], Ian T. Carroll [carroll.ian@gmail.com], Sydney K. Jones [syd@sevilleta.unm.edu], Andrew A. MacDonald [a.a.m.macdonald@gmail.com],  Dan F. B. Flynn [flynn@fas.harvard.edu], Peter Slaughter [slaughter@nceas.ucsb.edu], Julie Ripplinger [julie.ripplinger@asu.edu], Scott L. Collins [scollins@sevilleta.unm.edu], Corinna Gries [cgries@wisc.edu], Matthew B. Jones [jones@nceas.ucsb.edu]\n- Version 1.x: [doi:10.5063/F1542KJB](https://doi.org/10.5063/F1542KJB)\n- Version 2.x: [doi:10.5063/F1N877Z6](https://doi.org/10.5063/F1N877Z6)\n- **License**: [Apache 2](https://opensource.org/licenses/Apache-2.0)\n- [Package source code on Github](https://github.com/NCEAS/codyn)\n- [**Submit Bugs and feature requests**](https://github.com/NCEAS/codyn/issues)\n\nA package to analyze long-term ecological community datasets.\n\nUnivariate and multivariate temporal and spatial diversity indices, \nrank abundance curves, and community stability metrics. The functions \nimplement metrics that are either explicitly temporal and include the \noption to  calculate them over multiple replicates, or spatial and include \nthe option to calculate them over multiple time points. Functions fall into \nfive categories: static diversity indices, temporal diversity indices, \nspatial diversity indices, rank abundance curves, and community stability \nmetrics. The diversity indices are temporal and spatial analogs to \ntraditional diversity indices. Specifically, the package includes functions \nto calculate community richness, evenness and diversity at a given point in \nspace and time. In addition, it contains functions to calculate species \nturnover, mean rank shifts, and lags in community similarity between two \ntime points.\n\nFor an overview of __codyn__, see:\n    \n- Hallett LM, Jones SK, MacDonald AAA, Jones MB, Flynn DFB, Ripplinger J, Slaughter P, Gries C, Collins SL (2016) *codyn: An R package of community dynamics metrics.* Methods in Ecology and Evolution, 7(10):1146–1151. https://doi.org/10.1111/2041-210X.12569\n\nFor a description of the newer spatial methods in __codyn__ v2.x:\n\n- Avolio ML, Carroll IT, Collins SL, Houseman GR, Hallett LM, Isbell F, Koerner SE, Komatsu KJ, Smith MD, Wilcox KR (2019) *A comprehensive approach to analyzing community dynamics using rank abundance curves.* Ecosphere, 10(10):e02881. https://doi.org/10.1002/ecs2.2881\n\n\n## Installation\nFrom CRAN, the package can be installed using standard tools:\n```R\ninstall.packages(\"codyn\")\n```\n\n## Automated R CMD check with Docker via rhub\n\nTo simplify the process of running `R CMD check` on the package, one can easily run the build and tests using\nthe [`rhub`](https://github.com/r-hub/rhub) package. Use `rhub::platforms()` to get a list of platforms that can be used to build and test.\n\n```r\nlibrary(rhub)\nchks \u003c- check(platform = c(\"debian-gcc-devel\", \"fedora-gcc-devel\"), show_status = FALSE)\n```\n\nand the checks can be run locally using rhub as well using a docker container:\n\n```r\nlibrary(rhub)\nlocal_check_linux(image=\"rhub/fedora-gcc-devel\")\n```\n\n## Acknowledgments\n\nWork on this package was supported by NSF-ABI grant #1262458 to C. Gries, M. Jones, and S. Collins. Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California, and a SESYNC Synthesis Postdoctoral Fellowship to MLA.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnceas%2Fcodyn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnceas%2Fcodyn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnceas%2Fcodyn/lists"}